Gut microbiome alpha diversity decreases in relation to body weight, antibiotic exposure, and infection with multidrug-resistant organisms

The human gut microbiome is incredibly complex and critical for defense against pathogenic colonization, proper digestion, nutrient absorption, and regulation of both innate and adaptive immunity. Yet, patients are routinely given antibiotics that could permanently shift their gut microbiomes to a non-optimal state. Furthermore, infections with multidrug-resistant organisms (MDROs) may also lead to detrimental gut microbiome shifts in conjunction with shifts caused by the stronger antibiotics utilized to eliminate MDRO infections. These raw 16S rRNA gene sequencing data were generated from the fecal samples of 45 patients in order to assess gut microbiome shifts in response to antibiotic treatment and MDRO infection.